Months of protests have rocked Guinea over the constitutional reforms which critics fear will allow Conde to stay in power for a third term in the West Africa country.
Youths erected barricades, burned tyres and threw rocks at police who responded with tear gas in the opposition stronghold of Wanindara in the suburbs of the capital Conakry, witnesses said.
"Alpha, you have divided Guineans, time to go, thank you, enough," chanted a group of female protesters, dressed in the red of the opposition, who gathered in another Conakry area.
Similar clashes took place in Pita, 350 km (217 miles) north of Conakry, residents told AFP by telephone.
In the neighbouring Timbi-Madina, electoral material scheduled for Sunday's poll was destroyed on Wednesday, according to an official of the sub-prefecture.
The poll is deeply divisive. Critics say the constitutional referendum is a Trojan horse that would allow Conde to run for president again, overcoming current two-term limits.
Both the 2010 constitution and the new draft constitution limit presidential mandates to two terms.
But critics say a new constitution would mean a new republic, in effect resetting the presidential term counter to zero and allowing Conde to run again.
Conde, 81, says the reforms are needed to overhaul the constitution and usher in more progressive rights, especially those of women.
Since mid-October, people have taken to the streets to protest against the reforms.
At least 30 protesters have been killed in the demonstrations to date, as well as one gendarme.
Jailed under previous hardline regimes, Conde became Guinea's first democratically elected president in 2010.
He was returned to office by voters in 2015 for his second and final five-year term under the current constitution, but critics say he has become increasingly authoritarian.
Earlier this month he left the door open to running for a third term, saying there was "nothing more democratic" than the referendum on constitutional change.
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